rs1148259
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_052997.3(ANKRD30A):āc.3810A>Cā(p.Ala1270=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,609,586 control chromosomes in the GnomAD database, including 170,105 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.44 ( 15377 hom., cov: 31)
Exomes š: 0.45 ( 154728 hom. )
Consequence
ANKRD30A
NM_052997.3 synonymous
NM_052997.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.650
Genes affected
ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP7
?
Synonymous conserved (PhyloP=-0.65 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD30A | NM_052997.3 | c.3810A>C | p.Ala1270= | synonymous_variant | 34/36 | ENST00000361713.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD30A | ENST00000361713.2 | c.3810A>C | p.Ala1270= | synonymous_variant | 34/36 | 5 | NM_052997.3 | A2 | |
ANKRD30A | ENST00000374660.7 | c.4167A>C | p.Ala1389= | synonymous_variant | 40/42 | 5 | P4 | ||
ANKRD30A | ENST00000602533.7 | c.3810A>C | p.Ala1270= | synonymous_variant | 34/36 | 5 | A2 | ||
ANKRD30A | ENST00000696674.1 | c.543A>C | p.Ala181= | synonymous_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.445 AC: 67001AN: 150582Hom.: 15376 Cov.: 31
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GnomAD3 exomes AF: 0.497 AC: 122906AN: 247228Hom.: 32053 AF XY: 0.505 AC XY: 67842AN XY: 134256
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GnomAD4 exome AF: 0.453 AC: 660365AN: 1458886Hom.: 154728 Cov.: 67 AF XY: 0.461 AC XY: 334364AN XY: 725738
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GnomAD4 genome ? AF: 0.445 AC: 67027AN: 150700Hom.: 15377 Cov.: 31 AF XY: 0.452 AC XY: 33263AN XY: 73634
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at